fix samseq issue

likelet · Aug 29, 2018 · 2df9330 · 2df9330
1 parent fa63901
commit 2df9330
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Showing 4 changed files with 21 additions and 27 deletions.
diff --git a/inst/IDEA/GlobalFunction/PlotFunctions.R b/inst/IDEA/GlobalFunction/PlotFunctions.R
@@ -367,7 +367,7 @@ HeatmapData<-function(normalizedData,DEtable,DEmethod=c("DESeq","edgeR","NOIseq"
   }else if(DEmethod=='NOIseq'){
     DEtable<-DEtable[order(DEtable[,"prob"],decreasing = TRUE),]
   }else if(DEmethod=='SAMseq'){
-    DEtable<-DEtable[order(DEtable[,5]),]
+    DEtable<-DEtable[order(DEtable[,4]),]
   }
   DElist<-rownames(DEtable)
   if(length(DElist)>=Topnumber){

diff --git a/inst/IDEA/GlobalFunction/SAMseqAdjustFunction.R b/inst/IDEA/GlobalFunction/SAMseqAdjustFunction.R
@@ -19,20 +19,15 @@ library(samr)
 
 getsamfit<-function(data,conditionlist,myresp.type="Two class unpaired",mynperms = 100, mynresamp = 20, myfdr = 0.20){
   y=as.numeric(factor(conditionlist,labels = c(1:length(unique(conditionlist)))))
-  samfit <- SAMseq(data.matrix(data), y, resp.type =myresp.type,fdr.output=myfdr,geneid=row.names(data),genenames=row.names(data),nresamp = mynresamp,)
+  samfit <- SAMseq(data.matrix(data), y, resp.type =myresp.type,fdr.output=myfdr,geneid=row.names(data),genenames=row.names(data),nresamp = mynresamp)
 }
-getSamResultTable<-function(data,conditionlist,resp.type="Two class unpaired",myfdr=1){
-  #data must be rounded
-  #y must be a numberic vector
-  samfit <- getsamfit(data,conditionlist,myresp.type=resp.type,fdr=myfdr) 
-  result<-data.frame(samfit$siggenes.table$genes.up)
-  result2<-data.frame(samfit$siggenes.table$genes.lo)
-
-  return(rbind(result,result2))
-}
-
-samfitplot<-function(data,conditionlist,resp.type,myfdr=0.05){
-  samfit <- getsamfit(data,conditionlist,myresp.type=resp.type,fdr=myfdr)
-  plot(samfit)
+# getSamResultTable<-function(data,conditionlist,resp.type="Two class unpaired",myfdr=1){
+#   #data must be rounded
+#   #y must be a numberic vector
+#   samfit <- getsamfit(data,conditionlist,myresp.type=resp.type,fdr=myfdr) 
+#   result<-data.frame(samfit$siggenes.table$genes.up)
+#   result2<-data.frame(samfit$siggenes.table$genes.lo)
+#   
+#   return(rbind(result,result2))
+# }
 
-}
diff --git a/inst/IDEA/GlobalFunction/possionSeqDatafFunction.R b/inst/IDEA/GlobalFunction/possionSeqDatafFunction.R
@@ -24,6 +24,7 @@ getPossionTestResult<-function(data,condition,ispaired=FALSE){
   file.remove("PossionPow.txt")
   LL<-paralist()
   dat<-poissonData(data,condition,ispaired)
+  data<-data[complete.cases(data),]
   result<-PS.Main(dat,LL)
   return(result)
 }

diff --git a/inst/IDEA/server.R b/inst/IDEA/server.R
@@ -143,20 +143,18 @@ shinyServer(function(input,output,session){
         data=NULL
       })
     }
-
+    df <- NULL 
     if(values$wethernew=="example"){
-      example
+      df <- example
     }else{
       validate(
         need(!is.null(input$file1), "Please upload a data set")
       )
-      data
+      df <- data
     }
-    #     switch(values$wethernew,
-    #            'example'= example,
-    #            'upload'= data
-    #     )  
-
+    #remove gene with 0 count across samples 
+    df<-df[rowSums(df)>0,]
+   df
 
   })
 
@@ -1865,9 +1863,9 @@ getPowerCurve<-reactive({
 
   #SAMseq DE heatmap
   SAMseqHeatmapPlotfunction<-reactive({
-    table<-getresultPoissonSeqresultTableNew()
+    table<-getSAMseqresultTableNew()
     normalizedData<-normalizeDataNew()
-    data<-HeatmapData(normalizedData,table,DEmethod='PoissonSeq',Topnumber=input$SAMseqShowDeGenes)
+    data<-HeatmapData(normalizedData,table,DEmethod='SAMseq',Topnumber=input$SAMseqShowDeGenes)
     data
   })
   #SAMseq DE heatmap render
@@ -1917,7 +1915,7 @@ getPowerCurve<-reactive({
 
     content = function(file) {
       #Cairo(file=file, width = 600, height = 600,type = "png", units = "px", pointsize = 12, bg = "white", res = NA)
-      res<-getresultPoissonSeqresultTableNew()
+      res<-getSAMseqresultTableNew()
       write.csv(res,file=file)
     },
     contentType = 'text/csv'